rs12012519

Variant names:

• chrX-87935349-T-C
• rs12012519

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0484 in 111,678 control chromosomes in the GnomAD database, including 263 homozygotes. There are 1,527 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.048 (263 hom., 1527 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0483 AC: 5395 AN: 111622 Hom.: 263 Cov.: 23

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0144

Gnomad ASJ AF: 0.00642

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.00328

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00128

Gnomad OTH AF: 0.0350

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0484 AC: 5405 AN: 111678 Hom.: 263 Cov.: 23 AF XY: 0.0450 AC XY: 1527 AN XY: 33912

African (AFR) AF: 0.145 AC: 4441 AN: 30703

American (AMR) AF: 0.0144 AC: 151 AN: 10497

Ashkenazi Jewish (ASJ) AF: 0.00642 AC: 17 AN: 2649

East Asian (EAS) AF: 0.114 AC: 403 AN: 3545

South Asian (SAS) AF: 0.0945 AC: 252 AN: 2667

European-Finnish (FIN) AF: 0.00328 AC: 20 AN: 6098

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.00128 AC: 68 AN: 53080

Other (OTH) AF: 0.0346 AC: 53 AN: 1534

Alfa AF: 0.0226 Hom.: 1931

Bravo AF: 0.0541

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.38
PhyloP100		-0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12012519; hg19: chrX-87190349;